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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcgatgccatcttttccttctctccttgcgctacttttttttggtgtcattttgcaattatttttgtattctttggcgtgccagagttgtgctattgagcgaatgccgtggcttacaaaatcattatcacttgctgataattcggttacctcacagATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCTCCCATCTTTGCCAAGTTAAGCAAAGAGTACTCCGACATGGTTTTCCTCG

Basic information

species Physcomitrella patens
transcript PP1S98_9V6.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162203546|gb|FC380462.1|FC380462
EST:     CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATT                         ATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
genomic: CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATTgtaagagcga ... tacctcacagATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
EST: gi|162201227|gb|FC378462.1|FC378462
EST:     CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATT                         ATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
genomic: CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATTgtaagagcga ... tacctcacagATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
EST: gi|162203547|gb|FC380463.1|FC380463
EST:     CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATT                         ATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
genomic: CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATTgtaagagcga ... tacctcacagATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
EST: gi|162165368|gb|FC340843.1|FC340843
EST:     CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATT                         ATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
genomic: CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATTgtaagagcga ... tacctcacagATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
EST: gi|37849499|gb|BJ607507.1|BJ607507
EST:     CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATT                         ATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT
genomic: CGAAAGGTTTGGAGAATAAGCTGAACGAAGCTAAGGCCGCTGGTAAAATTgtaagagcga ... tacctcacagATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgccgtggcttacaaaatcattatcacttgctgataattcggttacctcacagATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCTCCCATCTTTGCCAAGTTAAGCAAAGAGTACTCCGACATGGTTTTCCTCG
                              tgctgat  putative branch site (score: 3)
                                            ttacctc  putative PPT
           ttacaaaatcattat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagcgatgccatcttttccttctctccttgcgctacttttttttggtgtcattttgcaattatttttgtattctttggcgtgccagagttgtgctattgagcgaatgccgtggcttacaaaatcattatcacttgctgataattcggttacctcacagATTGTCGTCGATTTTACTGCTACTTGGTGCAGCCCATGCCGAACGATGTCTCCCATCTTTGCCAAGTTAAGCAAAGAGTACTCCGACATGGTTTTCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG